Nordic Big Biomedical Data for Action. Davit Bzhalava, PhD Dept. of Laboratory Medicine, Karolinska Institutet, Sweden

Transcription

1 Nordic Big Biomedical Data for Action Davit Bzhalava, PhD Dept. of Laboratory Medicine, Karolinska Institutet, Sweden Davit Bzhalava

2 Nordic Center of Excellence in Health-Related e-sciences (NIASC) Davit Bzhalava

3 Main goals for NIASC Ø Overall aim: develop escience tools to improve health and societal preconditions for health Ø Develop and enhance risk prediction algorithms for risk of breast, prostate, colorectal and cervical cancer Ø Develop escience tools to enable implementation of riskstratified cancer screening polices à Establish the use of at least one escience-based predictive algorithm within a national screening program by program end in 2018 à Establish a significant legacy of escience tools as outlined below and later during today s discussion December 4,

4 The need for a Nordic concerted effort Ø Will achieve improved escience and improved translation to health policies through increased researcher mobility between Nordic countries, training and synergy effects Ø Joint development and sharing of escience tools, adapted to unique Nordic infrastructures (registers, biobanks and organised screening programs) Davit Bzhalava NIASC December 4,

5 NIASC IT/Bioinformaticians/DBA team Ø 4 IT/bioinformatician/DBAs were recruited in Norway, Sweden, Denmark and Finland. Ø In March 2015, the group had a meeting focusing on to get to know each other, to identify the most critical aspects for collaboration and to plan future activities. Davit Bzhalava

6 Nordic Workshop on Best Practices for Big Data Handling in Biobanking Ø Workshop brought together Nordic national biobanks, national biobank infrastructures, e-infrastructure service providers for sensitive data processing Ø Three working groups were formed that will: Formulate a joint use case on IT needs for the Nordic National Biobanks & Infrastructures. Develop and optimize useful bioinformatics softwares/algorithms that are scalable and able to efficiently utilize parallel computing Develop IT solutions that will enable mapping of multiple outcomes from registries to different biological entities (Reverse data mining or registromics ). Davit Bzhalava

7 Expected outcomes: Ø Design a use case for on Nordic Big Biomedical Data for Action Ø The NordForsk Nordic Colorectal Cancer consortium as an expansion towards a clinical use case exploiting the infrastructure. Ø To learn from each other (Where we are, what are the needs, how should we proceed) Ø Prepare for big data calls. Davit Bzhalava

8 Agenda day 1 Ø Session 1: Ø Data privacy regulation, ethics and legal issues Ø 13:00 13:40 The GDPR, balanced national legislation and exchange of data for research while still respecting national legislation. 13:40 14:00 Discussions Session 2: Nordic Colorectal Cancer consortium a use case for Synergy of NORDIC Big Biomedical Data Sources 14:00-14:25 Joakim Dillner Overview of the Nordic CRC Project 14:25-15:50 Karin Sundström Sweden Available resources and scientific interests of CRC Project 15:50-15:15 Frederik Trier Møller Acquisition of consumer data, storage, content and possibilities for CRC studies. Ø 15:15-15:30 Coffee Break Ø 15:30-15:50 Miriam Elfström NKCx, storage, content and possibilities for CRC studies. 15:50-16:15 Anu Jalanko Finnish Biobanks Available resources for CRC studies 16:15-16:40 Tõnu Esko Estonian Genome Center, Large scale population genomics and possibilities for CRC studies 16:40-17:05 Laufey Tryggvadóttir - Infrastructure and Potential Participation in Nordic CRC Poject. 17:05-17:30 E. Christina M. Wennerström - LABMED registry, storage, content and possibilities for CRC studies 18:00 Dinner Davit Bzhalava

9 Agenda day 2 Infrastructures and emerging technologies for processing big biomedical data 09:00-09:15 Davit Bzhalava Welcome, summary of day 1 and goals of the day 2 Ø Session 1: Data centers that could handle sensitive biomedical data in NIASC consortium 09:15 09:45 Antti Pursula - Tryggve: Nordic services for sensitive data. 09:45 10:15 Davit Bzhalava Biomedical Computing Center at KI 10:15 10:45 Jaakko Leinonen - epouta infrastructure 10:45 11:15 Joel Hedlund Tryggve2 planning: scopes and roadmap. 11:15 11:45 Discussions Ø 12:00-13:00 Lunch Ø Session 2: Emerging technologies for storing and processing big biomedical data Ø 13:00 13:30 Jim Dowling Hops Hadoop 13:30 14:00 Maarala Ilari Big Data processing for genomics. 14:00 14:30 Petri Klemelä -Delivering bioinformatics software as virtual machine image 14:30 15:00 Discussions 15:00-15:15 Coffee Break Davit Bzhalava

10 Agenda day 2 Session 3: Session algorithms for processing big biomedical data: 15:15 15:35 Piotr Bala PCJ BLAST 15:35 15:55 Raul Vicente Deep learning for computational biology 15:55 16:15 Davit Bzhalava genome assembly on distributed file system 16:15 16:35 Bartlomiej Wilkowski The Biobank Register: A search system for big biomedical and biobank data 16:35 17:00 Discussions 18:00 Dinner Davit Bzhalava

11 Agenda day 3 Ø Day 3 (09:00-12:00) 09:00-09:30 Eero Pukkala The Nordic Occupational Cancer Study (NOCCA), storage, content and possibilities for CRC studies. Ø Session 1: Software sustainability 09:30-10:00 Mike Croucher Is your research software correct? 10:00-10:30 Radovan Bast CodeRefinery 10:30-11:00 Discussions Ø Session 2: Plans for the future 11:00 11:30 Joakim Dillner Future work and upcoming big data calls 11:30 12:00 Discussions and planning for the future. Ø 12:00 13:00 Lunch Davit Bzhalava